Influenza neuraminidases hydrolyze the ketosidic linkage between N-acetylneuraminic acid and its adjacent galactose residue in sialosides. This enzyme is a tetrameric protein that plays a critical role in the release of progeny virions. Several methods have been described for the determination of neuraminidase activity, usually based on colorimetric, fluorescent, or chemiluminescent detection. However, only a few of these tests allow discrimination of the sialyl-linkage specificity (i.e., α2–3- versus α2–6-linked sialyllactosides) of the neuraminidase. Herein we report a glycoarray-based assay and a MALDI-TOF study for assessing the activity and specificity of two influenza neuraminidases on whole viruses. The human A(H3N2) and avian A(H5N2) neuraminidase activities were investigated. The results from both approaches demonstrated that α2–3 sialyllactoside was a better substrate than α2–6 sialyllactoside for both viruses and that H5N2 virus had a lower hydrolytic activity than H3N2.